PDB-9ii1: GH57 family Amylopullulanase mutant E256L from Aquifex aeolicus i...

ID or keywords:

Entry

Database: PDB / ID: 9ii1

Title

GH57 family Amylopullulanase mutant E256L from Aquifex aeolicus in complex with maltohexaose

Components

Glycoside hydrolase family 57 N-terminal domain-containing protein

Keywords

HYDROLASE / Amylopullulanase mutant E256L / Aquifex aeolicus / maltohexaose

Function / homology

Function and homology information

catalytic activity / carbohydrate metabolic process
Similarity search - Function

Biological species

Aquifex aeolicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.501 Å

Authors

Zhu, Z.M. / Wang, W.W. / Yu, F.

Funding support

China, 2items

Citation

Journal: Commun Biol / Year: 2025
Title: The crystal structure of GH57 family amylopullulanase reveals its dual binding pockets sharing the same catalytic dyad.
Authors: Zhu, Z. / Wang, W. / Li, M. / Xu, Q. / Zhou, H. / Huang, L. / Wang, Q. / Yu, F.

History

Deposition	Jun 18, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Jun 4, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ii1.cif.gz	422 KB	Display	PDBx/mmCIF format
PDB format	pdb9ii1.ent.gz	346.5 KB	Display	PDB format
PDBx/mmJSON format	9ii1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ii/9ii1 ftp://data.pdbj.org/pub/pdb/validation_reports/ii/9ii1	HTTPS FTP

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Related structure data

Related structure data	8zyiC 9ihtC 9ihuC 9ihvC 9ihwC 9ihxC 9ii0C 9k7cC 9k7dC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#24 - Dec 2001 Glycogen Phosphorylase similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (2)

Deposited unit

A: Glycoside hydrolase family 57 N-terminal domain-containing protein

B: Glycoside hydrolase family 57 N-terminal domain-containing protein

hetero molecules

118 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycoside hydrolase family 57 N-terminal domain-containing protein

hetero molecules

defined by author
Evidence: gel filtration
59.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glycoside hydrolase family 57 N-terminal domain-containing protein

hetero molecules

defined by author
58.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.831, 39.638, 193.778
Angle α, β, γ (deg.)	90.00, 95.76, 90.00
Int Tables number	3
Space group name H-M	P121

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Protein , 1 types, 2 molecules AB

#1: Protein	Glycoside hydrolase family 57 N-terminal domain-containing protein Mass: 57237.281 Da / Num. of mol.: 2 / Mutation: E256L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria) Gene: aq_720 / Production host: Escherichia coli (E. coli) / References: UniProt: O66934

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Sugars , 3 types, 4 molecules

#2: Polysaccharide

alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...

Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose

Descriptor	Type	Program
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1	WURCS	PDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}	LINUCS	PDB-CARE

#3: Polysaccharide

alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose

Descriptor	Type	Program
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1	WURCS	PDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}	LINUCS	PDB-CARE

#4: Polysaccharide

alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltotriose

Descriptor	Type	Program
DGlcpa1-4DGlcpa1-4DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}	LINUCS	PDB-CARE

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Non-polymers , 2 types, 554 molecules

#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.03 Å³/Da / Density % sol: 39.42 %
Crystal grow	Temperature: 338 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium citrate, pH 4.2, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 9, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.5→96.4 Å / Num. obs: 147906 / % possible obs: 100 % / Redundancy: 6.2 % / CC_1/2: 0.996 / R_merge(I) obs: 0.131 / R_pim(I) all: 0.056 / R_rim(I) all: 0.142 / Χ²: 0.79 / Net I/σ(I): 5.6 / Num. measured all: 922301
Reflection shell	Resolution: 1.5→1.58 Å / % possible obs: 99.8 % / Redundancy: 5.8 % / R_merge(I) obs: 1.645 / Num. measured all: 124942 / Num. unique obs: 21482 / CC_1/2: 0.45 / R_pim(I) all: 0.73 / R_rim(I) all: 1.804 / Χ²: 0.61 / Net I/σ(I) obs: 1.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.501→56.158 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2001	7221	4.89 %
R_work	0.171	-	-
obs	0.1724	147732	99.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.501→56.158 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8086	0	221	549	8856

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	8541
X-RAY DIFFRACTION	f_angle_d	1.081	11571
X-RAY DIFFRACTION	f_dihedral_angle_d	6.246	5083
X-RAY DIFFRACTION	f_chiral_restr	0.099	1255
X-RAY DIFFRACTION	f_plane_restr	0.007	1422

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.5013-1.5184	0.3456	236	0.3312	4632	X-RAY DIFFRACTION	98
1.5184-1.5362	0.3155	237	0.3178	4554	X-RAY DIFFRACTION	99
1.5362-1.555	0.3231	261	0.3036	4556	X-RAY DIFFRACTION	99
1.555-1.5746	0.3188	264	0.2844	4671	X-RAY DIFFRACTION	100
1.5746-1.5954	0.2848	232	0.2777	4653	X-RAY DIFFRACTION	100
1.5954-1.6172	0.3135	216	0.2625	4612	X-RAY DIFFRACTION	100
1.6172-1.6403	0.2901	240	0.2521	4665	X-RAY DIFFRACTION	100
1.6403-1.6648	0.2785	239	0.2421	4640	X-RAY DIFFRACTION	100
1.6648-1.6908	0.2556	249	0.232	4681	X-RAY DIFFRACTION	100
1.6908-1.7186	0.2551	261	0.2218	4638	X-RAY DIFFRACTION	100
1.7186-1.7482	0.2555	229	0.2115	4621	X-RAY DIFFRACTION	100
1.7482-1.78	0.2335	217	0.2104	4701	X-RAY DIFFRACTION	100
1.78-1.8142	0.2662	248	0.2105	4705	X-RAY DIFFRACTION	100
1.8142-1.8513	0.2402	283	0.1973	4595	X-RAY DIFFRACTION	100
1.8513-1.8915	0.2388	249	0.1821	4654	X-RAY DIFFRACTION	100
1.8915-1.9355	0.1958	230	0.1635	4652	X-RAY DIFFRACTION	100
1.9355-1.9839	0.2078	229	0.1619	4698	X-RAY DIFFRACTION	100
1.9839-2.0376	0.1932	267	0.157	4655	X-RAY DIFFRACTION	100
2.0376-2.0975	0.1974	216	0.1583	4747	X-RAY DIFFRACTION	100
2.0975-2.1652	0.2042	213	0.1636	4666	X-RAY DIFFRACTION	100
2.1652-2.2426	0.1835	234	0.1647	4687	X-RAY DIFFRACTION	100
2.2426-2.3324	0.1912	241	0.1542	4753	X-RAY DIFFRACTION	100
2.3324-2.4386	0.1985	246	0.1568	4651	X-RAY DIFFRACTION	100
2.4386-2.5671	0.1811	236	0.1573	4710	X-RAY DIFFRACTION	100
2.5671-2.728	0.1782	231	0.154	4708	X-RAY DIFFRACTION	100
2.728-2.9386	0.1929	237	0.1525	4742	X-RAY DIFFRACTION	100
2.9386-3.2343	0.1746	236	0.1505	4742	X-RAY DIFFRACTION	100
3.2343-3.7022	0.1474	284	0.1372	4721	X-RAY DIFFRACTION	100
3.7022-4.664	0.1509	224	0.1246	4817	X-RAY DIFFRACTION	100
4.664-56.158	0.1808	236	0.1599	4984	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.051	-0.1068	0.1836	0.6588	-0.1558	1.923	0.0605	-0.0473	-0.0974	-0.0519	-0.0041	0.0355	0.1198	0.0102	-0.05	0.0848	-0.0005	0.0047	0.0194	-0.0048	0.1159	15.7853	12.9211	70.1298
2	0.8888	-0.597	-1.0167	1.1033	0.8223	3.2769	-0.0035	-0.2408	-0.0394	0.1278	0.0322	0.0238	0.039	0.057	-0.0393	0.1257	-0.0005	-0.0249	0.2392	0.0098	0.1295	9.674	18.8584	91.1137
3	2.1829	-0.4547	-0.8971	1.1465	-0.1764	3.389	0.1097	-0.1897	0.2508	0.1118	-0.0037	0.1011	-0.5035	-0.4033	-0.0455	0.1401	0.0362	0.0303	0.1788	-0.0164	0.1857	0.0967	26.1926	82.5718
4	1.9872	-1.3107	-2.0634	2.0814	2.7541	5.149	-0.1176	-0.0839	-0.3091	0.0665	-0.0863	0.1604	0.4318	-0.322	0.219	0.1366	-0.03	-0.0122	0.0944	0.0257	0.1589	4.3364	8.5734	74.7209
5	2.1205	0.4205	0.9289	1.3201	0.1774	1.6467	0.0548	-0.0311	-0.082	0.0121	-0.0121	-0.1559	0.1135	0.2456	-0.0532	0.0984	0.0354	0.0182	0.124	-0.02	0.1129	34.8586	10.6956	69.5039
6	1.6754	-0.8176	-0.0141	1.1893	0.0802	1.3451	0.1004	0.1735	0.1083	-0.1745	-0.0724	-0.1172	-0.0453	0.1738	-0.0224	0.1253	-0.0105	0.0255	0.0775	-0.0075	0.1289	25.651	20.3193	56.0575
7	3.0234	-0.3971	-1.1168	1.6378	0.2383	3.1698	0.1298	0.3606	-0.1204	-0.3475	-0.0871	0.1113	-0.0703	-0.039	-0.0378	0.1551	0.0118	-0.031	0.0674	-0.0073	0.1163	12.9876	18.087	51.6893
8	1.2886	-0.1247	0.5535	1.6856	0.1693	3.6424	-0.0235	-0.0618	0.1481	0.0299	-0.0209	-0.1771	-0.2727	0.3303	0.0242	0.0369	-0.024	0.0236	0.1588	-0.0184	0.1831	38.8537	20.3058	72.071
9	5.0563	-0.9126	0.1582	3.8967	-0.2203	4.8124	-0.0224	-0.2867	0.0465	0.1625	0.0214	-0.0081	-0.0806	0.0772	-0.0198	0.0413	-0.0159	-0.016	0.149	-0.0143	0.0745	30.5979	15.8678	84.2937
10	1.3755	-0.0146	-0.3121	0.6333	-0.1724	2.4848	-0.0261	0.1868	-0.1062	0.0393	0.0001	-0.0421	0.0416	-0.0043	0.0167	0.0801	0.0204	-0.0137	0.0862	-0.0256	0.1128	0.1113	-4.9197	27.8908
11	1.7695	0.2703	-0.9963	0.7377	-0.4529	2.4965	0.0418	0.2295	0.136	-0.0376	-0.0363	-0.0733	-0.1199	0.2983	0.0215	0.1097	0.0137	-0.0149	0.2471	-0.001	0.1566	12.5362	0.4576	16.3598
12	1.4364	0.165	0.4571	0.4193	0.0016	1.593	0.0009	0.013	-0.0358	0.1129	0.0533	0.0675	-0.0679	-0.2391	-0.0316	0.1484	0.0552	0.0005	0.1289	-0.0128	0.1275	-14.4143	-2.3139	33.789
13	1.6385	0.1072	0.7016	0.5475	0.0132	2.0153	-0.0376	0.1959	0.0104	0.037	0.0343	0.0542	-0.1024	-0.1504	0.0002	0.0994	0.0277	-0.0013	0.1399	-0.0224	0.1298	-11.8102	-1.1605	24.3969

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 68 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 69 through 102 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 103 through 158 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 159 through 185 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 186 through 245 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 246 through 360 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 361 through 396 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 397 through 435 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 436 through 477 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 57 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 58 through 185 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 186 through 360 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 361 through 477 )

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